So the final portage of our journey, from Seed into Knife, is in Canada. Can we still legally use this portage considering the border is closed? Is this an issue for us?

You may use the portage legally, even under the present border closure.

You're good. Same with bottle portage, one around lower basswood falls, etc.

You can thank an old treaty that permits unrestricted usage of those portages that are right on the border. I believe it was the Webster–Ashburton Treaty of 1842 but it’s been quite a while since I read about it in Grace Lee Nute’s Minnesota history books.

Just keep a long paddle or canoe length between other parties :-)

And just remember not to use those portages for lunch spots or stop to fish - best get back in the US for those things.